Lateral gene transfer and the nature of bacterial innovation

Unlike eukaryotes, which evolve principally through the modification of existing genetic information, bacteria have obtained a significant proportion of their genetic diversity through the acquisition of sequences from distantly related organisms. Horizontal gene transfer produces extremely dynamic genomes in which substantial amounts of DNA are introduced into and deleted from the chromosome. These lateral transfers have effectively changed the ecological and pathogenic character of bacterial species.

[1]  N. Sueoka.  On the genetic basis of variation and heterogeneity of DNA base composition. , 1962, Proceedings of the National Academy of Sciences of the United States of America.

[2]  M. Riley,et al.  Evolution of the bacterial genome. , 1978, Annual review of microbiology.

[3]  P. Gemski,et al.  Presence of a virulence-associated plasmid in Yersinia pseudotuberculosis , 1980, Infection and immunity.

[4]  D. Portnoy,et al.  Characterization of plasmids and plasmid-associated determinants of Yersinia enterocolitica pathogenesis , 1981, Infection and immunity.

[5]  C. R. Weeks,et al.  The gene for type A streptococcal exotoxin (erythrogenic toxin) is located in bacteriophage T12 , 1984, Infection and immunity.

[6]  P. Sansonetti,et al.  Cloning of plasmid DNA sequences involved in invasion of HeLa cells by Shigella flexneri , 1985, Infection and immunity.

[7]  S. Falkow,et al.  A single genetic locus encoded by Yersinia pseudotuberculosis permits invasion of cultured animal cells by Escherichia coli K-12 , 1985, Nature.

[8]  100 years ago , 1985, Nature.

[9]  M. Santoro,et al.  A new oncogene in human thyroid papillary carcinomas and their lymph-nodal metastases , 1987, Nature.

[10]  S. Osawa,et al.  The guanine and cytosine content of genomic DNA and bacterial evolution. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[11]  V. Buchanan-Wollaston,et al.  The mob and oriT mobilization functions of a bacterial plasmid promote its transfer to plants , 1987, Nature.

[12]  M. P. Jackson,et al.  Nucleotide sequence analysis and comparison of the structural genes for Shiga-like toxin I and Shiga-like toxin II encoded by bacteriophages from Escherichia coli 933 , 1987 .

[13]  S. Goodman,et al.  Identification and arrangement of the DNA sequence recognized in specific transformation of Neisseria gonorrhoeae. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[14]  S. Makino,et al.  Virulence-associated genetic regions comprising 31 kilobases of the 230-kilobase plasmid in Shigella flexneri 2a , 1988, Journal of bacteriology.

[15]  J. Heinemann,et al.  Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast , 1989, Nature.

[16]  M. Radman,et al.  The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants , 1989, Nature.

[17]  M. Riley,et al.  The Bacterial Chromosome , 1990 .

[18]  A. Danchin,et al.  Evidence for horizontal gene transfer in Escherichia coli speciation. , 1991, Journal of molecular biology.

[19]  C. Elkins,et al.  Species-specific uptake of DNA by gonococci is mediated by a 10-base-pair sequence , 1991, Journal of bacteriology.

[20]  J. Sun,et al.  Association of a retroelement with a P4-like cryptic prophage (retronphage phi R73) integrated into the selenocystyl tRNA gene of Escherichia coli , 1991, Journal of bacteriology.

[21]  H. Ochman,et al.  Horizontal transfer of a phosphatase gene as evidence for mosaic structure of the Salmonella genome. , 1992, The EMBO journal.

[22]  C. Sasakawa,et al.  The absence of a surface protease, OmpT, determines the intercellular spreading ability of Shigella: the relationship between the ompT and kcpA loci , 1993, Molecular microbiology.

[23]  J. Hacker,et al.  Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen , 1994, Infection and immunity.

[24]  M. Katz,et al.  A role for bacteriophages in the evolution and transfer of bacterial virulence determinants , 1995, Molecular microbiology.

[25]  W. Rabsch,et al.  tRNA genes and pathogenicity islands: influence on virulence and metabolic properties of uropathogenic Escherichia coli , 1995, Molecular microbiology.

[26]  R M Hall,et al.  Mobile gene cassettes and integrons: capture and spread of genes by site‐specific recombination , 1995, Molecular microbiology.

[27]  H. Schmieger,et al.  Frequency of generalized transducing phages in natural isolates of the Salmonella typhimurium complex , 1995, Applied and environmental microbiology.

[28]  R. Fleischmann,et al.  Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome. , 1995, Science.

[29]  Matthew K. Waldor,et al.  Lysogenic Conversion by a Filamentous Phage Encoding Cholera Toxin , 1996, Science.

[30]  P. Reeves,et al.  Gene transfer is a major factor in bacterial evolution. , 1996, Molecular biology and evolution.

[31]  J R Roth,et al.  Selfish operons: horizontal transfer may drive the evolution of gene clusters. , 1996, Genetics.

[32]  Howard Ochman,et al.  Pathogenicity Islands: Bacterial Evolution in Quantum Leaps , 1996, Cell.

[33]  H. Ochman,et al.  Amelioration of Bacterial Genomes: Rates of Change and Exchange , 1997, Journal of Molecular Evolution.

[34]  J Hacker,et al.  Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution , 1997, Molecular microbiology.

[35]  I. Matic.  Rates of change and exchange , 1997 .

[36]  F. Taddei,et al.  Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[37]  E. Groisman,et al.  The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival , 1997, The EMBO journal.

[38]  H. Ochman,et al.  How Salmonella became a pathogen. , 1997, Trends in microbiology.

[39]  T. McDaniel,et al.  A cloned pathogenicity island from enteropathogenic Escherichia coli confers the attaching and effacing phenotype on E. coli K‐12 , 1997, Molecular microbiology.

[40]  R. Hall.  Mobile gene cassettes and integrons: moving antibiotic resistance genes in gram-negative bacteria. , 2007, Ciba Foundation symposium.

[41]  R. Novick,et al.  The gene for toxic shock toxin is carried by a family of mobile pathogenicity islands in Staphylococcus aureus , 1998, Molecular microbiology.

[42]  E V Koonin,et al.  Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. , 1998, Trends in genetics : TIG.

[43]  D. Mazel,et al.  A distinctive class of integron in the Vibrio cholerae genome. , 1998, Science.

[44]  C. Kurland,et al.  Reductive evolution of resident genomes. , 1998, Trends in microbiology.

[45]  E. Groisman.  The ins and outs of virulence gene expression: Mg2+ as a regulatory signal. , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

[46]  C. Bloch,et al.  "Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[47]  S. Karlin,et al.  Comparative DNA analysis across diverse genomes. , 1998, Annual review of genetics.

[48]  H. Ochman,et al.  Molecular archaeology of the Escherichia coli genome. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[49]  Saul A. Teukolsky,et al.  Black Holes , 1998 .

[50]  Sunny C. Jiang,et al.  Gene Transfer by Transduction in the Marine Environment , 1998, Applied and Environmental Microbiology.

[51]  S. Casjens,et al.  The diverse and dynamic structure of bacterial genomes. , 1998, Annual review of genetics.

[52]  S. Salzberg,et al.  Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima , 1999, Nature.

[53]  J. M. Smith,et al.  The detection and measurement of recombination from sequence data. , 1999, Genetics.

[54]  Sezgin Erdoğan,et al.  Environmental regulation of Salmonella pathogenicity island 2 gene expression , 1999, Molecular microbiology.

[55]  S. Vokes,et al.  The aerobactin iron transport system genes in Shigella flexneri are present within a pathogenicity island , 1999, Molecular microbiology.

[56]  R. L. Charlebois.  Organization of the Prokaryotic Genome , 1999 .

[57]  E V Koonin,et al.  Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. , 1999, Genome research.

[58]  John M. Logsdon,et al.  Evolutionary genomics: Thermotoga heats up lateral gene transfer , 1999, Current Biology.

[59]  Cécile Fairhead,et al.  Mitochondrial DNA repairs double-strand breaks in yeast chromosomes , 1999, Nature.

[60]  E. Groisman,et al.  The selC‐associated SHI‐2 pathogenicity island of Shigella flexneri , 1999, Molecular microbiology.

[61]  W. Rabsch,et al.  Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[62]  D. Maneval,et al.  A bacteriophage encoding a pathogenicity island, a type-IV pilus and a phage receptor in cholera bacteria , 1999, Nature.

[63]  J. Andersson,et al.  Insights into the evolutionary process of genome degradation. , 1999, Current opinion in genetics & development.

[64]  T. Gaasterland,et al.  Archaeal genomics : Genomics , 1999 .

[65]  Doolittle Wf.  Phylogenetic Classification and the Universal Tree , 1999 .

[66]  E V Koonin,et al.  Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange. , 1999, Trends in genetics : TIG.

[67]  J. Roth,et al.  Genomic Flux: Genome Evolution by Gene Loss and Acquisition , 1999 .

[68]  J. Lawrence.  Gene transfer, speciation, and the evolution of bacterial genomes. , 1999, Current opinion in microbiology.

[69]  D. Dubnau,et al.  DNA uptake in bacteria. , 1999, Annual review of microbiology.

[70]  J. Davison,et al.  Genetic exchange between bacteria in the environment. , 1999, Plasmid.

[71]  D. Mazel,et al.  Resistance gene capture. , 1999, Current opinion in microbiology.

[72]  T. Ohta.  Mechanisms of molecular evolution. , 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.